A variety of tools and methods exist for examining surface features and structure at the microscale and even nanoscale level. Scanning probe microscopy (SPM) allows for mapping surface topology at a microscale level by moving a detector tip carried at the free end of a cantilever beam over or across the surface of the material being mapped. This type of microscope may operate by direct physical contact with the surface (scanning atomic force microscopy or AFM) or, in a tunneling mode, by detection of a tunneling current when the tip is at selected distance from the surface (scanning tunneling microscopy or STM).
These types of devices have proven very useful for mapping surface topography, e.g., for detecting imperfections in integrated-circuit chips, but is not designed or can be operated to detect specific chemical compounds or chemical groups. This concept has been extended to parallel-high-speed AFM (e.g., Minne, 1998; 1999).
The scanning tip approach has also been adapted for optical detection of mapping of a surface. U.S. Pat. No. 6,441,359, for example, describes a near-field optical scanning system in which near-field optics is carried at the free end of a cantilever beam. The patent also discloses microfabrication methods for constructing an array of such optical elements for an optical scanning system. The tip to sample distance in the apparatus is controlled by an optical level deflection system that acts to maintain the top close to the sample surface. The system is able to achieve sub-wavelength resolution by scanning an aperture of sub-wavelength dimensions or by scanning the solid immersion lens very close to the sample. The device is not designed nor could it be used to detect individual chemical molecules or groups, die to the very low signal level that would be produced. Scanning near-filed optical microscopes (SNOM) have been proposed by others (e.g., Wolf).
One very sensitive probe for chemical analysis is surface-enhanced Raman spectroscopy or SERS (see, for example Kneipp). In addition SERS has been applied to a high-resolution scanning microscope for purposes of achieving high-resolution spectroscopic information from a sample surface, e.g., U.S. Pat. No. 6,002,471. The device includes a small conductive element (a plasmon resonance particle or PRP) at the free tip of a scanning cantilever beam, to enhance the light emitted in the vicinity of the probe. The sample substrate is formed of glass. The patent does not show or suggest methods for exploiting electromagnetic gap modes to enhance spectroscopic resolution that is likely for resolving single chemical structures, such as DNA bases, nor does the patent show of suggest a system capable of reading a plurality of samples, e.g., stretch DNA strands, in parallel.